One of Thompson's most controversial television appearances was on an episode of Star Trek: Deep Space Nine entitled "Rejoined". In the episode, she participated in one of US television's first same-sex kisses. The episode first aired on October 30, 1995. She made a guest appearance on Law and Order: SVU on October 7, 2003 in the season five episode "Mother", playing Dr. Greta Heints, a psychiatrist who rehabilitates sex offenders in order to prepare them for a return to society. She is attacked and knocked unconscious in the early scenes of the episode, and in the course of the investigation, Detectives Olivia Benson (Mariska Hargitay) and Elliot Stabler (Christopher Meloni) discover Heints has been accused of having a romantic relationship with one of her patients.

Thompson starred on the NBC series Kings, which was based on the biblical story of David.[6] She played Queen Rose Benjamin, an analogue of Ahinoam, the wife of Saul. The show premiered in March 2009 and ended in July. From 2012 to 2014 she played the role of Moira Queen in CW series Arrow.